Table II

Comparison of GPS 2.0 with previous prediction tools, including ScanSite, KinasePhos 1.0 and 2.0, NetPhosK, and pkaPS

Both the positive and negative data we tested for GPS 2.0 were submitted on these Web servers. And we fixed Sp to be similar with that used in previous tools to compare the Sn values. The performances with better values than those from GPS 2.0 are bold.

Predictors and thresholdPKAATMCDC2Src
SnSpSnSpSnSpSnSp
%%%%
ScanSite
    Low69.1495.0254.5593.6773.0895.1328.6895.28
    Medium42.4399.1727.2798.57 29.23 99.26 11.7699.37
    High 16.91 99.91 18.1899.70 8.46 99.84 3.6899.94
KinasePhos 1.0
    90%85.1690.6489.0983.8672.3186.3747.0689.93
    95%80.1294.5087.2789.7663.0892.6938.2493.91
    100%58.4698.4281.8296.04 48.46 97.99 25.0097.84
KinasePhos 2.055.1989.2089.0938.12 13.08 99.72 86.8655.97
NetPhosK77.7491.1885.4597.6016.9287.7933.0995.39
pkaPS89.6190.81
GPS 2.083.0995.04100.0094.0377.9695.1654.0295.34
49.2699.1772.7398.6223.1299.2617.2499.43
8.6199.9132.7399.707.5399.843.8399.93
89.9190.75a93.0186.4166.2889.96
84.5794.4989.7892.7157.0994.05
64.3998.4398.1896.0446.7797.9937.9397.85
91.6989.259.1499.7291.1956.03
89.6191.2687.2797.6191.9487.8452.8795.44
89.9190.91
  • a Not compared because both Sn and Sp of GPS 2.0 were better.